[Openchemistry-developers] Sample CSV data for mongochem?

[Marcus D. Hanwell]

On Tue, Feb 5, 2013 at 2:52 PM, Eric E. Monson <emonson at cs.duke.edu> wrote:
> Hey Kyle,
>
> I'm trying to get this to work, but I'm stuck trying to get data into the DB. When I do a CSV import, I only end up with the final molecule in the database, as if it's not generating new IDs as it goes, and is just overwriting the same data over and over for each molecule in the CSV file… I'll attach my CSV to see if there were any conversion problems from the SDF. I used the exact same string ("mass tpsa vabc rotatable-bonds") for the descriptor names as you suggested, so if there should have been other names listed, please tell me. (And, BTW, what is the File->Add New Data menu option supposed to do?)
>
We definitely need to make it easier to try MongoChem out! There is no
facility to turn Python wrapping on in the superbuild at this stage. I
exported out small test database, I don't see anything in there and it
is just a few of the PubChem molecules. I can push that somewhere, I
think it is around 10MB bzipped and you should just be able to use the
MongoDB import command.

I have been looking at issues such as long distance MongoDB too
(currently using MongoChem in France with a MongoDB hosted in Clifton
Park, NY - it is a little slow! Thanks for your notes - it looks like
getting MongoChem built was relatively painless, and most of your
issues were with getting Chemkit and its Python bindings to build - is
that correct?

We will be working on making all three applications easier to get up
and running, and demo. MongoChem presents a few special challenges of
its own due to needing a database. We may be able to host a read-only
demo instance of MongoDB for example, but then you hit latency issues.
It is very easy to copy a database to a local instance too at that
stage, or provide a few ready-made database dumps that could easily be
imported to get you started.

Thanks,

Marcus